Research workbench
Crystal structure of the P. abyssi exosome RNase pH ring complexed with udp and gmp
Analyse Crystal structure of the P. abyssi exosome RNase pH ring complexed with udp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PNZ
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable exosome complex exonuclease 1; Probable exosome complex exonuclease 2
- EC
- 3.1.13.-
- UniProt
- Q9V119, Q9V118
- Ligands
- UDP, 5GP
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 236 | 32% helix, 31% strand | Q9V119 |
| B | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 267 | 30% helix, 34% strand | Q9V118 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- 5GP · Guanosine-5'-monophosphate · ligand · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.55 | 0.82 | 19 | empty |
| 2 | 122 | 0.50 | 0.80 | 16 | empty |
| 3 | 126 | 0.44 | 0.77 | 25 | UDP |
Interfaces
1 interface between chains.
- A–B · 1195 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2PNZ · Crystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9V119 · AlphaFold monomer V2.0 prediction for exosome complex component RRP41 (Q9V119) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9V118 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (Q9V118) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9V119
- Every structure of UniProt Q9V118
- Elsewhere: RCSB PDB 2PNZ · PDBe 2PNZ · UniProt Q9V119 · UniProt Q9V118
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